I would think that since they are a drone/bot, the reason for the bounty is to make sure the Thargons (possibly in some as yet unseen sort of ship) don't recover them and re-use them. So it is disabling/destroying enemy equipment to prevent it being used that the cr and "kill" are for. Since a "kill" is given for removing obstacles (asteroids), it seems reasonable enough and consistent with even the Elite game's logic.
It may be too limiting to think of the score as one progresses to Elite status as *only* being for straightforward kills. Clearing pathways of asteroids (presumably to remove them as an obstacle/hazard) has always been work that was also apparently respected, so why not helping the Navy by mopping up after battles?
Think of it this way.. If a commander actually shot enough asteroids and Thargon drones so make it to "competent", well then they certainly would be pretty competent at using the laser at least.
Edit: They do still pose at least a potential threat. Since the recovered battle drones can be reprogrammed and used by the player, then logically the Thargons can reactivate them even easier. Now, if you want more risk involved in sitting around scrapping them, maybe if a Thargon patrol comes by and catches you at it, those inert drones suddenly could stop being inert. For every drone you kill in the resulting fight, they just activate another one so long as the supply lasts.
